YONR - BACSU - GREMLIN Contacts

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YONR - SPBc2 prophage-derived uncharacterized HTH-type transcriptional regulator YonR

UniProt:	O31943	Sequences: MFGERLKKCRTSKGYSQQRMADFLGITRQGYGKYEIGKAEPDLKTLTKLSNILGVSTDFLLKGTHAQFDLDEILNDPETLIAGYNGMISEEQAKELLYYLLKKEFEEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	108 (101)
Sequences:	1292 (1167)
Seq/√Len:	116.1

ECOLI - DICA YDCN
BACSU - YONR YQAE ANSR YOBD SLRR SINR XRE RGHRB RGHR IMMR YQAF YGZD YAZB
HALSA - O51961 Q9HRZ8

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_M	31_Y	3.338	1.00
18_Q	22_D	2.907	1.00
18_Q	28_R	2.875	1.00
10_R	35_E	2.715	1.00
51_N	63_G	2.633	1.00
15_Y	52_I	2.423	1.00
2_F	6_L	2.372	1.00
23_F	52_I	2.193	1.00
57_T	61_L	2.148	1.00
27_T	30_G	2.093	1.00
29_Q	33_K	2.092	1.00
89_S	92_Q	2.009	1.00
5_R	59_F	1.919	1.00
9_C	53_L	1.910	1.00
26_I	31_Y	1.888	1.00
40_E	43_L	1.866	1.00
33_K	38_K	1.865	1.00
3_G	37_G	1.853	1.00
99_Y	102_K	1.761	1.00
33_K	39_A	1.693	1.00
20_M	53_L	1.600	1.00
28_R	32_G	1.584	1.00
29_Q	32_G	1.502	1.00
95_E	102_K	1.491	1.00
30_G	33_K	1.473	1.00
20_M	49_L	1.375	1.00
58_D	63_G	1.352	1.00
95_E	99_Y	1.297	1.00
50_S	63_G	1.283	0.99
27_T	33_K	1.282	0.99
32_G	36_I	1.266	0.99
98_Y	102_K	1.254	0.99
6_L	31_Y	1.195	0.99
43_L	46_L	1.194	0.99
33_K	36_I	1.192	0.99
26_I	30_G	1.179	0.99
96_L	100_L	1.174	0.99
88_I	100_L	1.145	0.99
82_A	85_N	1.144	0.99
17_Q	28_R	1.134	0.99
15_Y	23_F	1.132	0.99
88_I	93_A	1.126	0.99
34_Y	45_T	1.119	0.99
2_F	43_L	1.079	0.98
12_S	67_Q	1.048	0.98
45_T	48_K	1.030	0.98
92_Q	95_E	1.018	0.97
5_R	63_G	1.013	0.97
46_L	61_L	1.005	0.97
55_V	59_F	0.999	0.97
5_R	62_K	0.966	0.96
28_R	36_I	0.966	0.96
2_F	46_L	0.964	0.96
5_R	65_H	0.958	0.96
97_L	100_L	0.943	0.96
46_L	57_T	0.943	0.96
95_E	98_Y	0.928	0.95
5_R	8_K	0.916	0.95
2_F	60_L	0.908	0.95
85_N	93_A	0.902	0.95
42_D	45_T	0.897	0.95
34_Y	39_A	0.884	0.94
15_Y	19_R	0.883	0.94
24_L	52_I	0.874	0.94
26_I	34_Y	0.866	0.93
81_I	87_M	0.852	0.93
19_R	22_D	0.852	0.93
81_I	84_Y	0.841	0.92
2_F	53_L	0.839	0.92
17_Q	21_A	0.830	0.92
19_R	23_F	0.821	0.92
24_L	49_L	0.817	0.91
9_C	55_V	0.816	0.91
28_R	33_K	0.816	0.91
41_P	58_D	0.803	0.91
40_E	45_T	0.785	0.90
13_K	23_F	0.776	0.89
4_E	37_G	0.774	0.89
27_T	39_A	0.769	0.89
81_I	85_N	0.762	0.88
17_Q	31_Y	0.762	0.88
24_L	53_L	0.754	0.88
20_M	52_I	0.754	0.88
97_L	101_L	0.751	0.88
92_Q	99_Y	0.748	0.87
20_M	24_L	0.744	0.87
34_Y	41_P	0.740	0.87
21_A	28_R	0.737	0.87
28_R	38_K	0.732	0.86
85_N	88_I	0.731	0.86
50_S	57_T	0.730	0.86
81_I	86_G	0.719	0.85
75_N	78_E	0.714	0.85
27_T	32_G	0.708	0.84
26_I	29_Q	0.706	0.84
21_A	29_Q	0.704	0.84
84_Y	93_A	0.703	0.84
40_E	44_K	0.692	0.83
25_G	48_K	0.692	0.83
92_Q	96_L	0.692	0.83
85_N	89_S	0.682	0.82
46_L	58_D	0.679	0.82
9_C	52_I	0.678	0.82
16_S	19_R	0.677	0.82
79_T	83_G	0.674	0.81
32_G	41_P	0.673	0.81
84_Y	97_L	0.662	0.80
48_K	51_N	0.659	0.80
76_D	80_L	0.655	0.79
28_R	31_Y	0.646	0.78
84_Y	87_M	0.639	0.78
83_G	87_M	0.637	0.77
15_Y	20_M	0.629	0.77
86_G	97_L	0.626	0.76
69_D	74_L	0.622	0.76
39_A	42_D	0.619	0.75
6_L	20_M	0.617	0.75
21_A	33_K	0.614	0.75
76_D	79_T	0.611	0.74
43_L	61_L	0.609	0.74
6_L	11_T	0.606	0.74
6_L	53_L	0.605	0.74
70_L	77_P	0.600	0.73
82_A	98_Y	0.599	0.73
32_G	39_A	0.598	0.73
7_K	10_R	0.583	0.71
94_K	98_Y	0.583	0.71
90_E	94_K	0.579	0.71
86_G	92_Q	0.577	0.70
27_T	38_K	0.557	0.68
67_Q	72_E	0.555	0.67
18_Q	32_G	0.555	0.67
95_E	100_L	0.542	0.65
85_N	99_Y	0.540	0.65
88_I	96_L	0.535	0.65
96_L	101_L	0.532	0.64
31_Y	34_Y	0.532	0.64
97_L	102_K	0.528	0.63
29_Q	38_K	0.526	0.63
89_S	95_E	0.526	0.63
30_G	40_E	0.524	0.63
77_P	80_L	0.520	0.62
92_Q	100_L	0.520	0.62
29_Q	36_I	0.516	0.62
78_E	93_A	0.513	0.61
43_L	47_T	0.513	0.61
21_A	31_Y	0.512	0.61
70_L	76_D	0.507	0.60
88_I	92_Q	0.506	0.60
22_D	25_G	0.504	0.60
96_L	102_K	0.500	0.59
71_D	74_L	0.500	0.59

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4ndwA	2	1	99.8	0.339	Contact Map
3r1fA	2	1	99.8	0.35	Contact Map
4o8bA	2	0.8981	99.8	0.355	Contact Map
4jcyA	2	0.8148	99.8	0.366	Contact Map
1b0nA	2	0.9259	99.8	0.374	Contact Map
3qwgA	2	0.6852	99.7	0.381	Contact Map
3op9A	4	0.9537	99.7	0.385	Contact Map
3ivpA	2	0.9537	99.7	0.393	Contact Map
2p5tA	2	0.3704	99.7	0.419	Contact Map
2ebyA	2	0.8981	99.7	0.429	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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